Cited in
(88)- Modeling for evolving biological networks with scale-free connectivity, hierarchical modularity, and disassortativity
- Operon prediction based on SVM
- A modified Ising model of Barabási-Albert network with gene-type spins
- Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea
- Characteristics of promoter architecture-dependent expression noise and bursting kinetics
- Computational prediction of conserved operons and phylogenetic footprinting of transcription regulatory elements in the metal-reducing bacterial family \textit{Geobacteraceae}
- A mixed-integer optimization framework for the synthesis and analysis of regulatory networks
- Bayesian Variational Inference for Exponential Random Graph Models
- A hybrid promoter analysis methodology for prokaryotic genomes
- Binding of transcription factors adapts to resolve information-energy tradeoff
- Modeling promoter search by \textit{E. coli} RNA polymerase: one-dimensional diffusion in a sequence-dependent energy landscape
- Gene regulatory networks. Methods and protocols
- Modeling and analysis of gene regulatory networks
- Embedding of biological regulatory networks and property preservation
- Mathematical conditions for induced cell differentiation and trans-differentiation in adult cells
- Ranking of network elements based on functional substructures
- SOLNP
- TRESNEI
- SIMoNe
- E-CELL
- EDISON
- G1DBN
- MetaCyc
- The recognition and prediction of \(\sigma^{70}\) promoters in \textit{Escherichia coli} K-12
- gNCA
- Footprinter
- BioProspector
- GGMselect
- HPAM
- SynTReN
- LTR_FINDER
- Netsim
- BiNGO
- CLENCH
- ARACNE
- PlantTFDB
- SIRENE
- bc3net
- WebLogo
- Information content based model for the topological properties of the gene regulatory network of \textit{Escherichia coli}
- Regulatory dynamics of standard two-component systems in bacteria
- JASPAR
- Matrix eQTL
- GeneNetWeaver
- GeneMarkS
- NARROMI
- BacPP
- ANAT
- BGRMI
- BioPreDyn-bench
- CopraRNA
- Diurnal
- DREM
- DINGO
- GeneSPIDER
- GeNGe
- IntaRNA
- IntScore
- LASSIE
- MMG
- NetBenchmark
- Netter
- Path2Models
- REDfly
- SGN Sim
- sgnesR
- SPINE
- SOSlib
- TRaCE+
- PSoL
- CplexA
- Dizzy
- Genome size and operon content
- PhyME
- GNA
- DREAM4
- REVEAL
- JDINAC
- Wilks' \(\Lambda \) dissimilarity measures for gene clustering: an approach based on the identification of transcription modules
- Fast computing global structural balance in signed networks based on memetic algorithm
- Computational challenges in systems biology
- Bayesian joint modeling of multiple gene networks and diverse genomic data to identify target genes of a transcription factor
- Directionality of real world networks as predicted by path length in directed and undirected graphs
- Effects of alternative connectivity on behavior of randomly constructed Boolean networks
- Dynamics of transcription of closely spaced promoters in \textit{Escherichia coli}, one event at a time
- Transcription factor binding sites detection by using alignment-based approach
- Constrained community-based gene regulatory network inference
- BacPP: bacterial promoter prediction -- a tool for accurate sigma-factor specific assignment in enterobacteria
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